Our team delivers OpenPrescribing.net, a publicly funded and openly accessible explorer for NHS primary care prescribing supported by prescribing data openly published by the NHS Business Services Authority.
We were concerned that the NHS did not share hospital medicines data in a similar manner to primary care and that it should be shared (see Goldacre and MacKenna 2020).
In September 2020 NHS BSA published hospital medicines data for the first time. We have prepared the following notebook for investigating the use of narcolepsy treatments in English hospitals.
If you have any feedback or insight The DataLab team can be contacted at ebmdatalab@phc.ox.ac.uk.
The file data/narcolepsy_meds.csv contains the SNOMED codes for the medicines we are investigating, see Table below with raw data. More information about each SNOMED code included in this analysis is shown in the methods section below (see dm+d Table). See the document codelists/create-codelists.Rmd for more information about how the codelist was created.
# Define vector with selected SNOMED codes for narcolepsy Treatments
codelist <- read_csv(here("data/narcolepsy-meds.csv"),
# convert to strings (they are stored as strings in SCMD table)
col_types = cols(id = col_character()))
# changed col type in read_csv function above
codes <- codelist$idcodelist %>%
reactable(filterable = TRUE,
columns = list(
type = reactable::colDef(minWidth = 40),
id = reactable::colDef(minWidth = 100),
bnf_code = reactable::colDef(minWidth = 100),
nm = reactable::colDef(minWidth = 200),
ingredient = reactable::colDef(minWidth = 100),
ddd = reactable::colDef(minWidth = 30)
),
style = list(fontSize = "12px"),
highlight = TRUE
)Before we can analyse trends and variation we need to prepare our dataset. This analysis uses three different sources of data. The file scipts/get_data.R describes the pre-processing of the “NHS Trusts” data (see below)
The NHS Digital “GP mapping file” which provides STP and region names mapped to STP and region ODS codes, published here.
The NHS Digital “Etr” file that maps trust organisation codes to trust names, STP ODS codes and region ODS codes, published here.
# Load ETR data
df_etr <- readr::read_csv(here::here("data/etr_tidy.csv")) %>%
select(c("ods_code", "ods_name", "region_code", "stp_code"))
# load older ETR data and find any additional codes here not in current list
df_etr_historic <- readr::read_csv(here::here("data/etr.csv"),
col_names = FALSE) %>%
select(1:4)
colnames(df_etr_historic) <- c("ods_code", "ods_name", "region_code", "stp_code")
df_etr_intersect <- intersect(df_etr$ods_code, df_etr_historic$ods_code)
df_etr_historic <- df_etr_historic %>%
dplyr::filter(!ods_code %in% df_etr_intersect)
df_etr <- rbind(df_etr, df_etr_historic)
# Load stp to regions data
stp_to_region_map <- read_csv(here::here("data/gp-reg-pat-prac-map.csv")) %>%
group_by(STP_CODE, STP_NAME) %>%
summarise(COMM_REGION_NAME = first(COMM_REGION_NAME),
COMM_REGION_CODE = first(COMM_REGION_CODE)) %>%
janitor::clean_names()
# check which STPs are in lookup table
stp_count <- df_etr %>%
group_by(stp_code) %>%
summarise(n = n(),
ods_code = first(ods_code),
ods_name = first(ods_name))
stp_count <- left_join(stp_count,
stp_to_region_map,
by = "stp_code")# Sustainability and Transformation Partnerships (STPs)
df_etr %>%
left_join(stp_to_region_map, by = "stp_code") %>%
select(ods_name, stp_name, comm_region_name) %>%
mutate(stp_name = fct_explicit_na(stp_name),
comm_region_name = fct_explicit_na(comm_region_name)) %>%
reactable::reactable(filterable = TRUE,
columns = list(ods_name = reactable::colDef(name = "Name",
minWidth = 200),
stp_name = reactable::colDef(name = "STP",
minWidth = 150),
comm_region_name = reactable::colDef(name = "Region",
minWidth = 70)),
style = list(fontSize = "12px"),
highlight = TRUE)data/df_scmd_narcolepsy.csv# Define SQL query for Secondary Care Medicines Data (SCMD) data
# Select variables and calculate quantity of medicines grouped by
# year_month, ods_code, vmp_snomed_code, vmp_snomed_name
sql_query_scmd <- dbplyr::sql("SELECT
year_month,
ods_code,
vmp_snomed_code,
vmp_product_name,
SUM(total_quanity_in_vmp_unit) AS total_quantity
FROM ebmdatalab.scmd.scmd
GROUP BY
year_month,
ods_code,
vmp_snomed_code,
vmp_product_name")# Secondary Care Medicines Data
# Connect to database, filter, and collect data.
# Get SCMD dataset
# db_scmd <- dplyr::tbl(conn_ebm_scmd, sql_query_scmd)
# Create dataframe for table
# df_scmd <- db_scmd %>%
# dplyr::filter(vmp_snomed_code %in% codes) %>%
# dplyr::collect()
# # Write csv file
# write_csv(df_scmd, here("data/df_scmd_narcolepsy.csv"))
# Read csv created above using bigquery database
df_scmd <- read_csv(here("data/df_scmd_narcolepsy.csv"),
col_types = cols(vmp_snomed_code = col_character()))# Tidy tidy tidy data
df_scmd_names <- df_scmd %>%
dplyr::left_join(dplyr::select(df_etr, ods_code, ods_name, stp_code), by = "ods_code") %>%
# some data cleaning as scmd uses some ods codes that are not up to date
mutate(stp_code = as.character(stp_code),
stp_code = case_when(
ods_code == "RQ6" ~ "QYG", # cheshire + merseyside
ods_code %in% c("RNL", "RE9", "RLN") ~ "QHM", # cumbria
ods_code %in% c("RM2", "RW3") ~ "QOP", # Mcr
ods_code == "RGQ" ~ "QJG", # Suffolk and North East Essex
ods_code == "RJF" ~ "QJ2", # Derbyshire
ods_code == "RR1" ~ "QHL", # Birmingham
ods_code == "R1J" ~ "QR1", # gloucestershire (trust present in data but wrong/old code)
ods_code == "R1E" ~ "QNC", # Staffs
ods_code == "TAD" ~ "QWO", # W Yorks
ods_code == "TAJ" ~ "QUA", # Black country
TRUE ~ stp_code)
)
check_missing <- select(df_scmd_names,c("ods_code", "ods_name", "stp_code")) %>%
distinct(.keep_all = TRUE)
check_missing <- check_missing[order(check_missing[["ods_name"]]), ]
# check which STPs are in data
scmd_stp_count <- df_scmd_names %>%
group_by(stp_code) %>%
summarise(n = n(),
ods_code = first(ods_code),
ods_name = first(ods_name))# Fill explicit missing and create dataset for sparkline in table
df_tab_sparkline <- df_scmd_names %>%
select(-c(vmp_product_name, ods_name, stp_code, stp_code, ods_name)) %>%
arrange(ods_code, vmp_snomed_code, year_month) %>%
as_tsibble(key = c(ods_code, vmp_snomed_code), index = year_month) %>%
fill_gaps(total_quantity = 0, .full = TRUE) %>%
tidyr::fill(.direction = "down") %>%
as_tibble() %>%
mutate(year_month = floor_date(year_month, unit = "month")) %>%
group_by(year_month, ods_code, vmp_snomed_code) %>%
arrange(ods_code, vmp_snomed_code, year_month) %>%
mutate(total_quantity = sum(total_quantity)) %>%
arrange(ods_code, vmp_snomed_code, year_month) %>%
distinct() %>%
group_by(ods_code, vmp_snomed_code) %>%
dplyr::summarise(count_sparkline = list(total_quantity)) %>%
group_by(ods_code, vmp_snomed_code) %>%
dplyr::mutate(total_quantity = sum(unlist(count_sparkline)))
# Create lookup datasets for joining
# SNOMED
vmp_snomed_names_lookup <- df_scmd_names %>%
select(vmp_snomed_code, vmp_product_name) %>%
dplyr::distinct()
# Trust
trust_names_lookup <- df_scmd_names %>%
select(ods_code, ods_name, stp_code) %>%
dplyr::distinct()
# Join data
df_tab_sparkline <- df_tab_sparkline %>%
ungroup() %>%
arrange(ods_code) %>%
left_join(trust_names_lookup, by = c("ods_code")) %>%
left_join(vmp_snomed_names_lookup, by = c("vmp_snomed_code")) %>%
mutate(count_box = count_sparkline)
# See the ?tippy documentation to learn how to customize tooltips
with_tooltip <- function(value, tooltip, ...) {
div(style = "text-decoration: underline; text-decoration-style: dotted; cursor: help",
tippy(value, tooltip, ...))
}
# Create table
df_tab_sparkline %>%
select(ods_name, vmp_product_name,vmp_snomed_code, count_sparkline, count_box, total_quantity,
-ods_code, -stp_code) %>%
reactable(filterable = TRUE,
defaultSorted = c("ods_name", "total_quantity"),
groupBy = c("ods_name"),
columns = list(
ods_name = reactable::colDef(name = "Trust",
minWidth = 200),
count_sparkline = colDef(name = "Trend",
header = with_tooltip("Trend",
"Note that the y axis cannot be compared across different entries."),
minWidth = 50,
cell = function(value, index) {
sparkline(df_tab_sparkline$count_sparkline[[index]])
}),
count_box = reactable::colDef(show = FALSE),
total_quantity = reactable::colDef(name = "Quantity",
minWidth = 50,
aggregate = "sum",
format = reactable::colFormat(digits = 0)),
vmp_product_name = reactable::colDef(name = "Product",
minWidth = 150,
cell = function(value, index) {
vmp_snomed_code <- paste0("SNOMED: ", df_tab_sparkline$vmp_snomed_code[index])
vmp_snomed_code <- if (!is.na(vmp_snomed_code)) vmp_snomed_code else "Unknown"
div(
div(style = list(fontWeight = 600), value),
div(style = list(fontSize = 10), vmp_snomed_code))
}
),
vmp_snomed_code = reactable::colDef(show = FALSE)
),
style = list(fontSize = "12px"),
highlight = TRUE
)data/df_dmd_info.csv# Define SQL query for Dictionary of Medicines and Devices (dm+d) information
# Rename some variables to match names across different queries (e.g., vmp_snomed_code)
sql_query_dmd_info <- dbplyr::sql("SELECT
CAST(a.id AS STRING) AS vmp_snomed_code,
a.nm AS vmp_product_name,
a.vtm AS vtmid,
j.nm AS vtmnm,
b.form AS form_cd,
c.descr AS form_descr,
a.df_ind AS df_ind_cd,
d.descr AS df_descr,
a.udfs,
e.descr AS udfs_descr,
f.descr AS unit_dose_descr,
g.strnt_nmrtr_val,
h.descr AS strnt_nmrtr_uom,
g.strnt_dnmtr_val,
i.descr AS strnt_dnmtr_descr,
a.bnf_code,
k.presentation AS bnf_presentation
FROM ebmdatalab.dmd.vmp AS a
LEFT JOIN ebmdatalab.dmd.dform AS b
ON a.id = b.vmp
LEFT JOIN ebmdatalab.dmd.form AS c
ON b.form = c.cd
LEFT JOIN ebmdatalab.dmd.dfindicator AS d
ON a.df_ind = d.cd
LEFT JOIN ebmdatalab.dmd.unitofmeasure AS e
ON a.udfs_uom = e.cd
LEFT JOIN ebmdatalab.dmd.unitofmeasure AS f
ON a.unit_dose_uom = f.cd
LEFT JOIN ebmdatalab.dmd.vpi AS g
ON a.id = g.vmp
LEFT JOIN ebmdatalab.dmd.unitofmeasure AS h
ON g.strnt_nmrtr_uom = h.cd
LEFT JOIN ebmdatalab.dmd.unitofmeasure AS i
ON g.strnt_dnmtr_uom = i.cd
LEFT JOIN ebmdatalab.dmd.vtm AS j
ON a.vtm = j.id
LEFT JOIN ebmdatalab.hscic.bnf AS k
ON a.bnf_code = k.presentation_code")# Uncomment to get data from bigquery and write csv
# db_dmd_info <- dplyr::tbl(conn_ebm_scmd, sql_query_dmd_info)
#
# df_dmd_info <- db_dmd_info %>%
# filter(vmp_snomed_code %in% codes) %>%
# collect()
#
# write_csv(df_dmd_info, here("data/df_dmd_info.csv"))
# Read the csv file
df_dmd_info <- read_csv(here("data/df_dmd_info.csv"),
col_types = cols(vmp_snomed_code = col_character()))We use information on the daily defined dose (DDD) of each medicine, so that the volume of each VMP can be compared directly once converted to DDDs. The WHO publish DDDs online.
# Define tibble with mg_per_ddd for join later
ddds <- select(codelist, c('nm', 'ddd')) %>%
drop_na('ddd')
# get additional DDDs sourced elsewhere
df_scmd_mg <- df_scmd_names %>%
left_join(df_dmd_info, by = c("vmp_snomed_code", "vmp_product_name")) %>%
left_join(ddds, by = c("vmp_product_name" = "nm")) df_scmd_mg %>%
select(vmp_snomed_code, vtmnm, form_descr, udfs, udfs_descr,
strnt_nmrtr_val, strnt_nmrtr_uom, strnt_dnmtr_val,strnt_dnmtr_descr,
ddd) %>%
distinct() %>%
reactable(filterable = TRUE,
columns = list(
vmp_snomed_code = reactable::colDef(name = "SNOMED",
minWidth = 100),
vtmnm = reactable::colDef(name = "Name",
minWidth = 100),
form_descr = reactable::colDef(name = "Form",
minWidth = 80),
# udfs is the VMP unit dose form strength
udfs = reactable::colDef(name = "Value",
minWidth = 40),
udfs_descr = reactable::colDef(name = "Unit",
minWidth = 40),
# strnt_nmrtr
strnt_nmrtr_val = reactable::colDef(name = "Numerator",
minWidth = 60,
format = colFormat(suffix = " mg")),
strnt_nmrtr_uom = reactable::colDef(show = FALSE),
# strnt_dnmtr
strnt_dnmtr_val = reactable::colDef(name = "Denominator",
minWidth = 60,
format = colFormat(suffix = " ml")),
strnt_dnmtr_descr = reactable::colDef(show = FALSE),
ddd = reactable::colDef(name = "mg/ddd",
minWidth = 50)),
columnGroups = list(
colGroup(name = "UDFS", columns = c("udfs", "udfs_descr")),
colGroup(name = "Strength", columns = c("strnt_nmrtr_val", "strnt_dnmtr_val"))
),
style = list(fontSize = "12px"),
highlight = TRUE)The final data cleaning step is to convert the volume from VMP quantity (as provided in the SCMD dataset) to volume in DDDs.
df_scmd_ddd <- df_scmd_mg %>%
mutate(volume_singles = total_quantity / udfs,
volume_mg_strength = volume_singles * if_else(is.na(strnt_dnmtr_val),
true = strnt_nmrtr_val,
false = strnt_nmrtr_val *
(udfs / strnt_dnmtr_val)),
volume_ddd = volume_mg_strength / ddd)temp_ggplot <- df_scmd_ddd %>%
group_by(year_month, vtmnm) %>%
summarise(volume_ddd = sum(volume_ddd)) %>%
ggplot(aes(x = year_month,
y = volume_ddd,
colour = vtmnm,
group = vtmnm)) +
geom_line(size = 1, alpha = 0.5) +
geom_point(aes(text = paste0("<b>Month:</b> ",
lubridate::month(year_month, label = TRUE), " ",
lubridate::year(year_month), "<br>",
"<b>Volume:</b> ", round(volume_ddd, 0), "<br>",
"<b>Medication:</b> ", vtmnm)), size = 2) +
scale_x_date(date_breaks = "4 month", date_labels = "%b %y") +
scale_colour_viridis_d() +
labs(x = NULL, y = "Defined Daily Dose",
colour = NULL) +
geom_vline(xintercept = as.numeric(as.Date("2020-03-31")),
color = "orange",
linetype = 2,
lwd = .5,
alpha = .5) +
theme(text = element_text(size = 12))
# temp_ggplot
plotly::ggplotly(temp_ggplot,
tooltip = "text") %>%
plotly::config(displayModeBar = FALSE)Figure. National prescribing of narcolepsy treatments over time.
df_scmd_ddd_map <- df_scmd_ddd %>%
left_join(stp_to_region_map, by = "stp_code")temp_ggplot <- df_scmd_ddd_map %>%
group_by(comm_region_name, year_month, vtmnm) %>%
summarise(volume_ddd = sum(volume_ddd)) %>%
mutate(comm_region_name = fct_explicit_na(comm_region_name)) %>%
ggplot(aes(x = year_month, y = volume_ddd,
colour = comm_region_name, group = comm_region_name)) +
geom_vline(xintercept = as.numeric(as.Date("2020-03-31")),
color = "orange",
linetype = 2,
lwd = .5,
alpha = .5) +
geom_line(size = 1, alpha = 0.5) +
geom_point(aes(text = paste0("<b>Month:</b> ",
lubridate::month(year_month, label = TRUE), " ",
lubridate::year(year_month), "<br>",
"<b>Region:</b> ", comm_region_name, "<br>",
"<b>Volume:</b> ", round(volume_ddd, 0), "<br>",
"<b>Medication:</b> ", vtmnm)),
size = 2) +
scale_x_date(date_breaks = "4 month", date_labels = "%b %y") +
scale_colour_viridis_d(end = 1) +
labs(x = NULL,
y = "Defined Daily Dose",
colour = NULL) +
facet_wrap(~vtmnm, ncol = 1) +
theme(text = element_text(size = 12))
# temp_ggplot
plotly::ggplotly(temp_ggplot,
tooltip = "text") %>%
plotly::config(displayModeBar = FALSE)Figure. Regional prescribing of narcolepsy treatments over time.
temp_ggplot <- df_scmd_ddd_map %>%
select(year_month, ods_code, vtmnm, volume_ddd, comm_region_name) %>%
mutate(comm_region_name = fct_explicit_na(comm_region_name)) %>%
group_by(comm_region_name, vtmnm) %>%
summarise(volume_ddd = sum(volume_ddd)) %>%
group_by(comm_region_name) %>%
mutate(prop_use = volume_ddd / sum(volume_ddd, na.rm = TRUE),
pos = cumsum(volume_ddd) - volume_ddd/2,
total = sum(volume_ddd), na.rm = TRUE) %>%
ungroup() %>%
mutate(comm_region_name = fct_reorder(comm_region_name, total)) %>%
ggplot(aes(comm_region_name)) +
geom_bar(aes(y = volume_ddd,
fill = vtmnm,
text = paste0("<b>Region:</b> ", comm_region_name, "<br>",
"<b>Total volume in ddd:</b> ", round(total, 0), "<br>",
# "<b>Medication:</b> ", vtmnm, "<br>",
"<b>", vtmnm , " volume in ddd (%):</b> ", round(volume_ddd, 0), " (", scales::percent(prop_use, accuracy = 0.1), ")"
)
),
stat='identity',
# position = position_dodge()
) +
scale_fill_viridis_d() +
labs(subtitle = paste0("From: ", min(df_scmd_ddd_map$year_month), " to ", max(df_scmd_ddd_map$year_month)),
x = NULL,
y = "Defined Daily Dose",
fill = NULL) +
scale_y_continuous(labels = scales::comma) +
theme(text = element_text(size = 12)) +
coord_flip()
# temp_ggplot
plotly::ggplotly(temp_ggplot,
tooltip = "text") %>%
plotly::config(displayModeBar = FALSE)Figure. Total regional prescribing of narcolepsy treatments.
df_scmd_ddd_map_temp <- df_scmd_ddd_map %>%
# filter(year_month >= as.Date("2019-08-01") & year_month <= as.Date("2020-07-01")) %>%
select(year_month, ods_code, vtmnm, volume_ddd, stp_name) %>%
mutate(stp_name = fct_explicit_na(stp_name)) %>%
group_by(stp_name, vtmnm) %>%
summarise(volume_ddd = sum(volume_ddd)) %>%
group_by(stp_name) %>%
mutate(prop_use = volume_ddd / sum(volume_ddd, na.rm = TRUE),
pos = cumsum(volume_ddd) - volume_ddd/2,
total = sum(volume_ddd, na.rm = TRUE)) %>%
ungroup() %>%
mutate(rank = dense_rank(-total),
stp_name = fct_reorder(stp_name, -rank))
temp_ggplot <- df_scmd_ddd_map_temp %>%
filter(rank <= 20) %>%
ggplot(aes(stp_name)) +
geom_bar(aes(y = volume_ddd,
fill = vtmnm,
text = paste0("<b>STP:</b> ", stp_name, "<br>",
"<b>Total volume in ddd:</b> ", round(total, 0), "<br>",
"<b>", vtmnm , " volume in ddd:</b> ", round(volume_ddd, 0), " (", scales::percent(prop_use, accuracy = 0.1), ")")),
stat = 'identity') +
scale_fill_viridis_d() +
labs(subtitle = paste0("From: ", min(df_scmd_ddd_map$year_month), " to ", max(df_scmd_ddd_map$year_month)),
x = NULL,
y = "Defined Daily Dose",
fill = NULL) +
scale_y_continuous(labels = scales::comma) +
theme(text = element_text(size = 12),
legend.position = "bottom") +
coord_flip()
# temp_ggplot
plotly::ggplotly(temp_ggplot,
tooltip = "text") %>%
plotly::config(displayModeBar = FALSE) %>%
layout(legend = list(orientation = "h", x = -0.5, y =-.15))Figure. Total prescribing of narcolepsy treatments for 20 STPs with the largest volume across all selected medications.
# Create table, code here: "scripts/create_tables.R"
# the data is defined above and needs to contain the following columns:
# - stp_name <fct>
# - vtmnm <chr>
# - volume_ddd <dbl>
# - prop_use <dbl>
# - pos <dbl>
# - total <dbl>
# - rank <int>
create_med_use_table(data = df_scmd_ddd_map_temp)